rs2058112

chr12-1752992-G-Achr12-1752992-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(ADIPOR2):c.-86-1266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,040 control chromosomes in the GnomAD database, including 1,527 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1527 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

Genes affected

ADIPOR2 (HGNC:24041): (adiponectin receptor 2) The adiponectin receptors, ADIPOR1 (MIM 607945) and ADIPOR2, serve as receptors for globular and full-length adiponectin (MIM 605441) and mediate increased AMPK (see MIM 602739) and PPAR-alpha (PPARA; MIM 170998) ligand activities, as well as fatty acid oxidation and glucose uptake by adiponectin (Yamauchi et al., 2003 [PubMed 12802337]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR2	NM_024551.3	c.-86-1266G>A		intron_variant		ENST00000357103.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-86-1266G>A		intron_variant		1	NM_024551.3	P1
ADIPOR2	ENST00000537545.1	n.145-1266G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20329 AN: 151922 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20339 AN: 152040 Hom.: 1527 Cov.: 32 AF XY: 0.130 AC XY: 9695 AN XY: 74314

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0907

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.0753

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.128

Alfa AF: 0.122 Hom.: 2420

Bravo AF: 0.135

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.7
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2058112; hg19: chr12-1862158;